Join overlapping objects/meshes into one surface in Blender
I would use the boolean modifier to union them together.

Lets say I have 3 overlapping spheres i want to make into one, connected object.


Select one sphere, and create two boolean modifiers, both set to Union, with the other spheres as the objects:


Hit apply, and you can now delete the original two spheres. the third sphere with the boolean modifiers should now be one mesh that makes up all 3 spheres: